[gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

[Nikolay Alemasov]

Thank you, Mark!

     It was already tried. I mean a fresh unpacking and further cmake 
run. As for your first thought concerning a loss of access to some parts 
of gmxlib:
> [alemasov at nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ | grep -e "-" | 
> cut -d' ' -f 1 | sort -n | uniq
> drwxr-x---
> -rw-r-----

     So there are only two permissions patterns which allow me to 
read/write items in the directory. I am little bit confused. Are there 
any limitations about OS or cmake versions? The latter is "cmake version 
2.8.12".

> (Redirected from gmx-developers)
>
> The only way I can reproduce those symptoms is if I delete (or otherwise
> make unreadable) various parts of src/gmxlib. You may have deleted some
> files or been a different user at some point. I suggest you do a fresh
> unpack of the tarball and try again.
>
> Mark
>
>
> On Wed, Oct 16, 2013 at 7:19 AM, Nikolay Alemasov <such3r at gmail.com  <http://lists.gromacs.org/mailman/listinfo/gmx-users>> wrote:
>
> >/  Greetings,
> />/
> />/      I am trying to compile the source code v.4.6.3 with cmake. The shell
> />/  script is (ran from the "build" directory inside gromacs source root dir):
> />/
> />/   CC=/ifs/opt/2013/intel/bin/icc
> />>/  CXX=/ifs/opt/2013/intel/bin/**icpc
> />>/  CMAKE_PREFIX_PATH="/ifs/home/**bionet/alemasov/libraries/**fftw"
> />>/
> />>/  cmake .. \
> />>/  -DGMX_GPU=OFF \
> />>/  -DGMX_CPU_ACCELERATION=SSE2 \
> />>/  -DFFTWF_LIBRARY='/ifs/home/**bionet/alemasov/libraries/**fftw/lib/libfftw3f.so'
> />>/  \
> />>/  -DFFTWF_INCLUDE_DIR='/ifs/**home/bionet/alemasov/**libraries/fftw/include'
> />>/  \
> />>/  -DCMAKE_INSTALL_PREFIX='/ifs/**home/bionet/alemasov/**libraries/gromacs'
> />>/
> />/
> />/  And get a message (successful part was cut):
> />/  ...
> />/
> />>/  -- Performing Test HAVE_DLOPEN
> />>/  -- Performing Test HAVE_DLOPEN - Success
> />>/  -- Checking for dlopen - found
> />>/  -- Found the ability to use plug-ins when building shared libaries, so
> />>/  will compile to use plug-ins (e.g. to read VMD-supported file formats).
> />>/  -- Checking for suitable VMD version
> />>/  -- VMD plugins not found. Path to VMD can be set with VMDDIR.
> />>/  CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
> />>/    list sub-command REMOVE_ITEM requires two or more arguments.
> />>/
> />>/
> />>/  CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
> />>/    list sub-command REMOVE_ITEM requires two or more arguments.
> />>/
> />>/
> />>/  You have called ADD_LIBRARY for library md without any source files. This
> />>/  typically indicates a problem with your CMakeLists.txt file
> />>/  -- Configuring incomplete, errors occurred!
> />>/  See also "/ifs/home/bionet/alemasov/**libraries/gromacs-4.6.3/build/**
> />>/  CMakeFiles/CMakeOutput.log".
> />>/  See also "/ifs/home/bionet/alemasov/**libraries/gromacs-4.6.3/build/**
> />>/  CMakeFiles/CMakeError.log".
> />>/
> />/
> />/  Below is a content of the src/gmxlib/CMakeLists.txt:99-**105:
> />/
> />>/  99 : # Files called xxx_test.c are test drivers with a main() function
> />>/  for module xxx.c,
> />>/  100: # so they should not be included in the library
> />>/  101: file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
> />>/  102: list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
> />>/  103: # Selection has test_ instead of _test.
> />>/  104: file(GLOB SELECTION_TEST selection/test*)
> />>/  105: list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
> />>/
> />/
> />/  The target system:
> />/
> />/   Linux nks-g6.sscc.ru 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009
> />>/  x86_64 x86_64 x86_64 GNU/Linux
> />>/  Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> />>/  model name    : Intel(R) Xeon(R) CPU           X5560  @ 2.80GHz
> />>/
> />/
> />/  Please help me to sort out the issue. In fact my primary aim was to build
> />/  GPU-version of the GROMACS, but I can not do it even for the simplest
> />/  variant.
> />/  --
> />/  gmx-developers mailing list
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> />/  .
> />